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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAGgtttgctgctatctcacagtgaatctcatggtgcaacctttggtaactatgggttagtaactattttctgtaatgttttgatctgtgcag

Basic information

species Zea mays
transcript GRMZM2G014788_T01
intron # 26
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014788_T01 (Zea mays), 5'ss of exon 26
lower sequence: LOC_Os01g19470.1 (Oryza sativa), 5'ss of exon 26
GAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAGgtttgctgctatctcacagtgaatctcatggtgc-aacctttggtaactatgggt-tagtaactattttctgtaatgtt---ttgatctgtgcag
||| | || ||||| || || ||||| |||||||| |||||||| ||| ||||| |||| ||||| |||||||||||  ||||| | |||| || ||| |||| || | ||| |   |  | ||||    ||| |  | ||||   | || |    |||||   |  ||
GAATTAACTCCAGCCCCTGTATTTCCTCTTATTGTCGGAGTTTCCGTGATTGCATTGGTCATCAGCATGCCAAGgttc-ctgctctatcactgtaaatttcattgttctaacttgaagccattatgatcataggagttgttttaactgatatgacattgatgcttttag
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|211519911|gb|FL453783.1|FL453783
EST:     CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAG                         GTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
genomic: CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAGgtttgctgct ... atctgtgcagGTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
EST: gi|33092001|gb|CF051995.1|CF051995
EST:     CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAG                         GTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
genomic: CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAGgtttgctgct ... atctgtgcagGTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
EST: gi|211361549|gb|FL423686.1|FL423686
EST:     CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAG                         GTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
genomic: CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAGgtttgctgct ... atctgtgcagGTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
EST: gi|211041954|gb|FL378891.1|FL378891
EST:     CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAG                         GTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
genomic: CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAGgtttgctgct ... atctgtgcagGTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
EST: gi|60357426|gb|DN224399.1|DN224399
EST:     CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAG                         GTTAAATGACTTATACCAGAGCGCTGTAGGGATAACTTCTCTGGGTTCAGG
genomic: CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAGgtttgctgct ... atctgtgcagGTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
EST: gi|32928505|gb|CF033317.1|CF033317
EST:     CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAG                         GTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
genomic: CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAGgtttgctgct ... atctgtgcagGTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
EST: gi|5608456|gb|AI902033.1|AI902033
EST:     CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAG                         GTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
genomic: CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAGgtttgctgct ... atctgtgcagGTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
EST: gi|33091614|gb|CF051608.1|CF051608
EST:     CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAG                         GTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
genomic: CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAGgtttgctgct ... atctgtgcagGTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
EST: gi|32848978|gb|CD988659.1|CD988659
EST:     CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAG                         GTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
genomic: CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAGgtttgctgct ... atctgtgcagGTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
EST: gi|32942753|gb|CF047572.1|CF047572
EST:     CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAG                         GTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
genomic: CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAGgtttgctgct ... atctgtgcagGTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
EST: gi|32908270|gb|CF013083.1|CF013083
EST:     CCGCTTATTGTTGGAGTTTCTGTGGTTGTACTGGTGATCAGTATGCCAAG                         GTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
genomic: CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAGgtttgctgct ... atctgtgcagGTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
EST: gi|32933415|gb|CF038227.1|CF038227
EST:     CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAG                         GTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
genomic: CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAGgtttgctgct ... atctgtgcagGTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
EST: gi|32908269|gb|CF013082.1|CF013082
EST:     CCGCTTATTGTTGGAGTTTCTGTGGTTGTACTGGTGATCAGTATGCCAAG                         GTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
genomic: CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAGgtttgctgct ... atctgtgcagGTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
EST: gi|60399625|gb|DN232435.1|DN232435
EST:     CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAG                         GTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
genomic: CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAGgtttgctgct ... atctgtgcagGTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
EST: gi|67041526|gb|CO467781.1|CO467781
EST:     CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAG                         GTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
genomic: CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAGgtttgctgct ... atctgtgcagGTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
EST: gi|211516406|gb|FL409520.1|FL409520
EST:     CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAG                         GTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
genomic: CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAGgtttgctgct ... atctgtgcagGTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
EST: gi|211413951|gb|FL082391.1|FL082391
EST:     CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAG                         GTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
genomic: CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAGgtttgctgct ... atctgtgcagGTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
EST: gi|211441921|gb|FL415411.1|FL415411
EST:     CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGTCAAG                         GTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGGTCAGG
genomic: CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAGgtttgctgct ... atctgtgcagGTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
EST: gi|37383469|gb|CF628751.1|CF628751
EST:     CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAG                         GTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
genomic: CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAGgtttgctgct ... atctgtgcagGTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
EST: gi|6056869|gb|AW091274.1|AW091274
EST:     CCGCTTATTGTTGGAGTTTCTGTGGTTGCCCTGGTGATCAGTATGCCAAG                         GTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
genomic: CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAGgtttgctgct ... atctgtgcagGTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
EST: gi|6020513|gb|AW065441.1|AW065441
EST:     CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAG                         GTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
genomic: CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAGgtttgctgct ... atctgtgcagGTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
EST: gi|60346132|gb|DN213105.1|DN213105
EST:     CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAG                         GTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
genomic: CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAGgtttgctgct ... atctgtgcagGTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
EST: gi|32932418|gb|CF037230.1|CF037230
EST:     CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAG                         GTTAAATGACTTATACCGGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
genomic: CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAGgtttgctgct ... atctgtgcagGTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
EST: gi|5819266|gb|AI987472.1|AI987472
EST:     CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAG                         GTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG
genomic: CCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAGgtttgctgct ... atctgtgcagGTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 199

GAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAGgtttgctgct ... atctgtgcagGTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGGGATGGCACCGACCAAAAAGGAGCCACGCAAGAATATATTAAGAAAGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 161

GAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAGgtttgctgct ... atctgtgcagGTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGGGATGGCACCGACCAAAAAGGAGCCACGCAAGAATATATTAAGAAAGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 173

GAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAGgtttgctgct ... atctgtgcagGTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGGGATGGCACCGACCAAAAAGGAGCCACGCAAGAATATATTAAGAAAGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 129

GAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAGgtttgctgct ... atctgtgcagGTTAAATGACTTATACCAGAGCGCTGTAGGGATGACTTCTCTGGGTTCAGGGATGGCACCGACCAAAAAGGAGCCACGCAAGAATATATTAAGAAAGAGA


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACTGACCCCAGCACCAGTTTTTCCGCTTATTGTTGGAGTTTCTGTGGTTGCACTGGTGATCAGTATGCCAAGgtttgctgctatctcacagtgaatctcatggtgcaacctttggtaactatgggttagtaactattttctgtaatgttttgatctgtgcag

- - - - - - - - - - - - - - - - - TTGGAG